NM_005609.4:c.2009C>A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_005609.4(PYGM):c.2009C>A(p.Ala670Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A670V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005609.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYGM | ENST00000164139.4 | c.2009C>A | p.Ala670Glu | missense_variant | Exon 17 of 20 | 1 | NM_005609.4 | ENSP00000164139.3 | ||
PYGM | ENST00000377432.7 | c.1745C>A | p.Ala582Glu | missense_variant | Exon 15 of 18 | 2 | ENSP00000366650.3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152190Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Cov.: 32
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
Glycogen storage disease, type V Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at